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9z05

Structure of human lymphoid-specific helicase HELLS in its auto-inhibitory state (D3)

Method: ELECTRON MICROSCOPY Dmax: 124.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lymphoid-specific helicase

Homo sapiens

UniProt Q9NRZ9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–838 Chain B； UniProt 1–838 Chain C； UniProt 1–838 Chain D； UniProt 1–838 Chain E； UniProt 1–838 Chain F； UniProt 1–838 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 2.86 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9Z05 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8SKZ Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome Deposited 2023-04-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 500–553（54 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9Z04 Structure of human lymphoid-specific helicase HELLS in its auto-inhibitory state Deposited 2025-10-31 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Chain E 1–838（838 aa）
Chain F 1–838（838 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.99 Å
9Z06 Structure of human lymphoid-specific helicase HELLS in its auto-inhibitory state Deposited 2025-10-31 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Chain E 1–838（838 aa）
Chain F 1–838（838 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.39 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HELLS_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–838； UniProt 1–838 Author chain B； PDBConstruct 1–838； UniProt 1–838 Author chain C； PDBConstruct 1–838； UniProt 1–838 Author chain D； PDBConstruct 1–838； UniProt 1–838 Author chain E； PDBConstruct 1–838； UniProt 1–838 Author chain F； PDBConstruct 1–838； UniProt 1–838

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9z05

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9z05
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9z05
Deposition date deposition_date2025-10-31
Structure title titleStructure of human lymphoid-specific helicase HELLS in its auto-inhibitory state (D3)
Keywords keywordslymphoid-specific helicase, SF2 chromatin remodeler, ICF syndrome, ATP-binding, Chromatin-binding, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.49 Å
Radius of gyration Rg (electron density) rg_electron41.31 Å
Forward intensity I(0) i0723136000.00
Molecular weight molecular_weight225900.0 kDa
Excluded volume excluded_volume284860 ų
Envelope volume envelope_volume379560 ų
Hydration-shell volume shell_volume75289 ų
Envelope diameter envelope_diameter134.5 Å
Shell Rg shell_rg48.25 Å
Envelope Rg envelope_rg40.48 Å
Shape Rg shape_rg41.29 Å
Total Rg total_rg41.72 Å
Total atoms total_atoms15882
Residues n_residues1944
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax124.5 Å
Rg (real space) rg_real41.35 Å
Rg uncertainty (real space) rg_real_error0.91 Å
I(0) (real space) i0_real7.2310e+08
I(0) uncertainty (real space) i0_real_error1.3940e+07
Rg (reciprocal space) rg_reciprocal41.49 Å
I(0) (reciprocal space) i0_reciprocal723200000.0000
Solution quality estimate total_estimate0.8792
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary— Å
Skewness Skewness skewness0.200
Kurtosis Kurtosis kurtosis-0.567
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha136400000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.967; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.533
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)